Targeting gene amplification in cancer using triplex formation as a therapeutic strategy

ABSTRACT

Disclosed herein are methods and agents for the treatment of cancer using p53-independent apoptosis to reduce the number of p53-depleted or p53-mutated cancer cells that have amplified HER2 gene. Also disclosed herein are methods and agents for the treatment of HER2-positive cancer in individuals with Li-Fraumeni Syndrome.

RELATED APPLICATIONS

This application claims the benefit under 35 U.S.C. § 119(e) of U.S.provisional application Ser. No. 62/767,279, filed Nov. 14, 2018, thecontent of which is incorporated by reference herein in its entirety.

GOVERNMENT SUPPORT

This invention was made with government support under R21CA185192 andR01GM126211 awarded by the National Institutes of Health. The governmenthas certain rights in the invention.

BACKGROUND

Gene amplification often leads to higher expression of genes involved innormal cell growth and survival pathways^(1,2). As such, geneamplification is a major mechanism driving oncogenesis in a broadspectrum of cancers, ultimately affecting tumor progression and clinicaloutcome^(3,4). Several drugs have been developed to inhibit theoncogenic activity of amplified driver genes⁵. The majority of thesecancer therapeutics target the overexpressed protein products and theirclinical efficacy is often hampered by drug resistance^(6,7).

SUMMARY

Described herein is a novel therapeutic method for the treatment ofcancers that are characterized by gene amplification, and, in oneembodiment specifically, the treatment of cancers that are characterizedby HER2 gene amplification. In the method, manipulation of the DNAdamage response with triplex-forming oligonucleotides (TFOs) drivesp53-independent tumor-specific induction of apoptosis. The methoddescribed is particularly applicable to p53-independent cancers, whichare often aggressive and resistant to traditional chemotherapeuticdrugs. This provides a new and specific approach in targeted cancertherapy, which can have enormous impact on the field of precisionmedicine.

Accordingly, one aspect of the present disclosure provides a method ofreducing, in a population of cells, the number of p53-depleted cancercells in which a HER2 gene is amplified, the method comprisingcontacting p53-depleted cancer cells with triplex formingoligonucleotides (TFOs) targeted to a polypurine target site in theamplified-HER2 gene, under conditions under which the TFOs enter thep53-depleted cancer cells in sufficient quantity to induce apoptosis. Insome embodiments, the p53-depleted cells are mammalian cells. In someembodiments, the p53-depleted cells are human cells. In someembodiments, the polypurine target site is/comprises SEQ ID NO: 1, SEQID NO: 2, SEQ ID NO:5 or SEQ ID NO:6. In some embodiments, the TFOs areat least 13 nucleotides in length. In some embodiments, the TFOs are atleast 22 nucleotides in length. In some embodiments, at least 13 of thenucleotides hybridize to SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:5 or SEQID NO:6.

TFOs can be administered individually (e.g., all TFOs administered havethe same sequence) or a combination of two or more TFOs can beadministered (e.g., TFOs administered comprise different nucleotidesequences). In some embodiments, the TFOs comprise a nucleotide sequenceat least 90% identical to SEQ ID NO: 3; a nucleotide sequence at least90% identical to SEQ ID NO: 4; a nucleotide sequence at least 90%identical to SEQ ID NO: 7; a nucleotide at least 90% identical to SEQ IDNO: 8; or a combination of two, three or four of the foregoing. Forexample, TFOs administered can comprise a nucleotide sequence at least90% identical to SEQ ID NO: 3 and a nucleotide sequence at least 90%identical to SEQ ID NO: 4; a nucleotide sequence at least 90% identicalto SEQ ID NO: 3 and a nucleotide sequence at least 90% identical to SEQID NO: 7; a nucleotide sequence at least 90% identical to SEQ ID NO: 3and a nucleotide at least 90% identical to SEQ ID NO: 8; a nucleotidesequence at least 90% identical to SEQ ID NO: 4 and a nucleotidesequence at least 90% identical to SEQ ID NO: 7; a nucleotide sequenceat least 90% identical to SEQ ID NO: 4 and a nucleotide sequence atleast 90% identical to SEQ ID NO:8; a nucleotide sequence at least 90%identical to SEQ ID NO: 7 and a nucleotide sequence at least 90%identical to SEQ ID NO: 8.

In some embodiments, three different TFOs are administered. For example,the following can be administered:

-   a TFO that comprises a nucleotide sequence at least 90% identical to    SEQ ID NO: 3, a TFO that comprises a nucleotide sequence at least    90% identical to SEQ ID NO: 4 and a TFO that comprises a nucleotide    sequence at least 90% identical to SEQ ID NO: 7;-   a TFO that comprises a nucleotide sequence at least 90% identical to    SEQ ID NO: 3, a TFO that comprises a nucleotide sequence at least    90% identical to SEQ ID NO: 4 and a TFO that comprises a nucleotide    sequence at least 90% identical to SEQ ID NO: 8;-   a TFO that comprises a nucleotide sequence at least 90% identical to    SEQ ID NO: 3, a TFO that comprises a nucleotide sequence at least    90% identical to SEQ ID NO: 7 and a TFO that comprises a nucleotide    sequence at least 90% identical to SEQ ID NO: 8; or-   a TFO that comprises a nucleotide sequence at least 90% identical to    SEQ ID NO: 4, a TFO that comprises a nucleotide sequence at least    90% identical to SEQ ID NO: 7 and a TFO that comprises a nucleotide    sequence at least 90% identical to SEQ ID NO: 8.

In further embodiments, four different TFOs are administered: a (atleast one) TFO that comprises a nucleotide sequence at least 90%identical to SEQ ID NO: 3; a (at least one) TFO that comprises anucleotide sequence at least 90% identical to SEQ ID NO: 4; a (at leastone) TFO that comprises a nucleotide sequence at least 90% identical toSEQ ID NO: 7; and a (at least one) TFO that comprises a nucleotide atleast 90% identical to SEQ ID NO: 8.

Alternatively, TFOs that comprise a nucleotide sequence identical to SEQID NO: 3; TFOs that comprise a nucleotide sequence identical to SEQ IDNO: 4; TFOs that comprise a nucleotide sequence identical to SEQ ID NO:7; and TFOs that comprise a nucleotide sequence identical to SEQ ID NO:8 can be administered individually (e.g., all TFOs administered have thesame sequence) or a combination of two or more TFOs can be administered(e.g., TFOs administered comprise different nucleotide sequences).

For example, TFOs administered can comprise a nucleotide sequenceidentical to SEQ ID NO: 3 and a nucleotide sequence identical to SEQ IDNO: 4; a nucleotide sequence identical to SEQ ID NO: 3 and a nucleotidesequence identical to SEQ ID NO: 7; a nucleotide sequence identical toSEQ ID NO: 3 and a nucleotide sequence identical to SEQ ID NO: 8; anucleotide sequence identical to SEQ ID NO: 4 and a nucleotide sequenceidentical to SEQ ID NO: 7; a nucleotide sequence identical to SEQ ID NO:4 and a nucleotide sequence identical to SEQ ID NO:8; a nucleotidesequence identical to SEQ ID NO: 7 and a nucleotide sequence identicalto SEQ ID NO: 8.

In some embodiments, three different TFOs are administered. For example,the following can be administered:

-   a TFO that comprises a nucleotide sequence identical to SEQ ID NO:    3, a TFO that comprises a nucleotide sequence identical to SEQ ID    NO: 4 and a TFO that comprises a nucleotide sequence identical to    SEQ ID NO: 7;-   a TFO that comprises a nucleotide sequence identical to SEQ ID NO:    3, a TFO that comprises a nucleotide sequence identical to SEQ ID    NO: 4 and a TFO that comprises a nucleotide sequence identical to    SEQ ID NO: 8;-   a TFO that comprises a nucleotide sequence identical to SEQ ID NO:    3, a TFO that comprises a nucleotide sequence identical to SEQ ID    NO: 7 and a TFO that comprises a nucleotide sequence identical to    SEQ ID NO: 8; or-   a TFO that comprises a nucleotide sequence identical to SEQ ID NO:    4, a TFO that comprises a nucleotide sequence identical to SEQ ID    NO: 7 and a TFO that comprises a nucleotide sequence identical to    SEQ ID NO: 8.

In further embodiments, four different TFOs are administered: a (atleast one) TFO that comprises a nucleotide sequence identical to SEQ IDNO: 3; a (at least one) TFO that comprises a nucleotide sequenceidentical to SEQ ID NO: 4; a (at least one) TFO that comprises anucleotide sequence identical to SEQ ID NO: 7; and a (at least one) TFOthat comprises a nucleotide identical to SEQ ID NO: 8.

In some embodiments, the triplex forming oligonucleotides (TFOs) are ina delivery vehicle or are conjugated to a delivery vehicle. In someembodiments, the delivery vehicle is lipid nanoparticles. In someembodiments, the TFOs have backbone modifications. In some embodiments,the backbone modifications include phosphorothioates,phosphorodithioates, methylphosphonates, phosphoramidates,boranophosphate oligos, polyamides, methylene(methylimino) linkages,morpholino oligos, or some combination thereof. In some embodiments, thep53-depleted cancer cells are renal cell carcinoma cells, lung cancercells, colon cancer cells, colon carcinoma cells, ovarian cancer cells,breast cancer cells, colorectal cancer cells, gastric cancer cells,and/or endometrial cancer cells.

Another aspect of the present disclosure provides a method of reducing,in a population of cells, the number of p53-mutated cancer cells inwhich a HER2 gene is amplified, the method comprising contactingp53-mutated cancer cells with triplex forming oligonucleotides (TFOs)targeted to a polypurine site in the amplified-HER2 gene, underconditions under which the TFOs enter the p53-mutated cancer cells insufficient quantity to induce apoptosis. In some embodiments, thep53-mutated cells are mammalian cells. In some embodiments, thep53-mutated cells are human cells. In some embodiments, the polypurinetarget site is SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:5 or SEQ ID NO:6.In some embodiments, the TFOs are at least 13 nucleotides in length. Insome embodiments, the TFOs are at least 22 nucleotides in length. Insome embodiments, at least 13 of the nucleotides hybridize to SEQ ID NO:1, SEQ ID NO: 2, SEQ ID NO:5 or SEQ ID NO:6. In some embodiments, theTFOs comprise a nucleotide sequence at least 90% identical to SEQ ID NO:3, and/or a nucleotide sequence at least 90% identical to SEQ ID NO: 4,and/or a nucleotide sequence at least 90% identical to SEQ ID NO: 7and/or a nucleotide at least 90% identical to SEQ ID NO: 8. In someembodiments, the TFOs are in a delivery vehicle or are conjugated to adelivery vehicle. In some embodiments, the delivery vehicle is lipidnanoparticles. In some embodiments, the TFOs have backbonemodifications. In some embodiments, the backbone modifications includephosphorothioates, phosphorodithioates, methylphosphonates,phosphoramidates, boranophosphate oligos, polyamides,methylene(methylimino) linkages, morpholino oligos, or some combinationthereof. In some embodiments, the p53-mutated cancer cells are renalcell carcinoma cells, lung cancer cells, colon cancer cells, coloncarcinoma cells, ovarian cancer cells, breast cancer cells, colorectalcancer cells, gastric cancer cells, and/or endometrial cancer cells.

Another aspect of the present disclosure provides a method of treatingcancer in an individual with Li-Fraumeni syndrome, the method comprisingadministering to the individual TFOs targeted to a polypurine targetsite in an amplified-HER2 gene, under conditions under which the TFOsenter p53-depleted cancer cells in sufficient quantity to induceapoptosis. In some embodiments, the polypurine target site is SEQ ID NO:1, SEQ ID NO: 2, SEQ ID NO:5 or SEQ ID NO:6. In some embodiments, theTFOs are at least 13 nucleotides in length. In some embodiments, theTFOs are at least 22 nucleotides in length. In some embodiments, atleast 13 of the nucleotides hybridize to SEQ ID NO: 1, SEQ ID NO: 2, SEQID NO:5 or SEQ ID NO:6. In some embodiments, the TFOs comprise anucleotide sequence at least 90% identical to SEQ ID NO: 3, and/or anucleotide sequence at least 90% identical to SEQ ID NO: 4, and/or anucleotide sequence at least 90% identical to SEQ ID NO: 7 and/or anucleotide at least 90% identical to SEQ ID NO: 8. In some embodiments,the TFOs are in a delivery vehicle or are conjugated to a deliveryvehicle. In some embodiments, the delivery vehicle is lipidnanoparticles. In some embodiments, the TFOs are encapsulated in thelipid nanoparticles. In some embodiments, the TFOs have backbonemodifications. In some embodiments, the backbone modifications includephosphorothioates, phosphorodithioates, methylphosphonates,phosphoramidates, boranophosphate oligos, polyamides, methylene(methylimino) linkages, morpholino oligos, or some combination thereof.In some embodiments, the TFOs are administered by injection. In someembodiments, the TFOs are administered intratumorally orintraperitoneally. In some embodiments, an anticancer agent that is nota TFO is administered with the TFOs.

In some embodiments, the anticancer agent is a protein, a nucleic acid,a small molecule, or a drug. In some embodiments, the anticancer agentis a protein, a nucleic acid, a small molecule, or a drug.

Another aspect of the present disclosure provides a method ofadministering TFOs for the treatment of cancer, the method comprisingpreparing a mixture of TFOs targeted to a polypurine target site in anamplified-HER2 gene and administering the mixture of TFOs to anindividual, in sufficient quantity to induce p53-independent apoptosis.In some embodiments, the mixture of TFOs is encapsulated in lipidnanoparticles. In some embodiments, the polypurine target site is SEQ IDNO: 1, SEQ ID NO: 2, SEQ ID NO:5 or SEQ ID NO:6. In some embodiments,the TFOs are at least 13 nucleotides in length. In some embodiments, theTFOs are at least 22 nucleotides in length. In some embodiments, atleast 13 of the nucleotides hybridize to SEQ ID NO: 1, SEQ ID NO: 2, SEQID NO:5 or SEQ ID NO:6. In some embodiments, the mixture of TFOscomprises a nucleotide sequence at least 90% identical to SEQ ID NO: 3,and/or a nucleotide sequence at least 90% identical to SEQ ID NO: 4,and/or a nucleotide sequence at least 90% identical to SEQ ID NO: 7and/or a nucleotide at least 90% identical to SEQ ID NO: 8. In someembodiments, the TFOs have backbone modifications. In some embodiments,the backbone modifications include phosphorothioates,phosphorodithioates, methylphosphonates, phosphoramidates,boranophosphate oligos, polyamides, methylene(methylimino) linkages,morpholino oligos, or some combination thereof. In some embodiments, themixture of TFOs is administered by injection. In some embodiments, themixture of TFOs is administered intratumorally or intraperitoneally. Insome embodiments, an anticancer agent that is not a TFO is administeredwith the mixture of TFOs. In some embodiments, the anticancer agent is aprotein, a nucleic acid, a small molecule, or a drug. In someembodiments, the individual is a mammal. In some embodiments, theindividual is a human. In some embodiments, the individual is a model ofcancer. In some embodiments, the cancer is a carcinoma, a sarcoma or amelanoma with HER-2 gene amplification. In some embodiments, the modelof cancer is selected from a group including a p53-knockout mouse, aLi-Fraumeni Syndrome mouse, a mouse with MDA-MB-453 cells, SKBR3 cells,BT474 cells, PEO1 cells, SKOV3 cells, and p53-knockout mouse.

Another aspect of the present disclosure provides a composition,comprising TFOs targeted to a polypurine target site in anamplified-HER2 gene in sufficient quantity to induce p53-independentapoptosis in a p53-depleted cancer cell or a p53-mutated cancer cell, apharmaceutically acceptable carrier, and optionally lipid nanoparticles,wherein the TFOs are encapsulated in the lipid nanoparticles or areconjugated to the lipid nanoparticles. In some embodiments, thepolypurine target site is SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:5 or SEQID NO:6. In some embodiments, the TFOs are at least 13 nucleotides inlength. In some embodiments, the TFOs are at least 22 nucleotides inlength. In some embodiments, at least 13 of the nucleotides hybridize toSEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:5 or SEQ ID NO:6. In someembodiments, the TFOs comprise a nucleotide sequence at least 90%identical to SEQ ID NO: 3, and/or a nucleotide sequence at least 90%identical to SEQ ID NO: 4, and/or a nucleotide sequence at least 90%identical to SEQ ID NO: 7 and/or a nucleotide at least 90% identical toSEQ ID NO: 8. In some embodiments, the TFOs have backbone modifications.In some embodiments, the backbone modifications includephosphorothioates, phosphorodithioates, methylphosphonates,phosphoramidates, boranophosphate oligos, polyamides,methylene(methylimino) linkages, morpholino oligos, or some combinationthereof. In some embodiments, the pharmaceutically acceptable carriercomprises water or saline.

The details of one or more embodiments of the invention are set forth inthe description below. Other features or advantages of the presentinvention will be apparent from the drawings and detailed description ofseveral embodiments, and also from the appended claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentdisclosure, which can be better understood by reference to one or moreof these drawings in combination with the detailed description ofspecific embodiments presented herein. It is to be understood that thedata illustrated in the drawings in no way limit the scope of thedisclosure. In the drawings:

FIGS. 1A-1E include diagrams showing targeting of gene amplification incancer via triplex formation. FIG. 1A: a schematic illustration showinga drug design scheme. Targeting the HER2 gene on a genomic level usingDNA-binding molecules provides a novel therapeutic option to directlymanipulate the DNA damage response pathways to specifically attack theHER2-amplified tumor. Triplex-induced DNA damage will only provokeapoptosis when multiple triplex structures are formed, while nucleotideexcision repair (NER)-dependent repair prevails in the presence of oneor two structures. FIG. 1B: a table showing the gene copy numbercharacteristics of breast cancer cells lines ¹⁸. FIG. 1C: a photoshowing the western blot analysis of HER2 protein levels in breastcancer cell lines with varying gene copy number. FIG. 1D: a schematicillustration showing that TFOs bind as third strands in asequence-specific manner within the major groove of duplex DNA atpolypurine sites. The specificity of these molecules arises from theformation of base triplets via reverse Hoogsteen hydrogen bonds betweenthe third strand and the polypurine strand of the duplex DNA. Resultsshown are from the use of TFOs HER2-1 and HER2-205, designed to bind toa polypurine sequence located either in the promoter or the codingregion of the HER2 gene. FIG. 1E: photos of non-denatured metaphasechromosome spreads of MCF7 and BT474 breast cancer cells demonstratechromosomal binding of TAMRA-HER2-205 (red) to its target site locatedon chromosome (chr.) 17 (green).

FIGS. 2A-2H include diagrams showing that triplex induced DNA damage andapoptosis correlate with gene copy number. “UT”=untreated cells.“Mock”=cells with transfection reagent only. “MIX24”=cells treated withcontrol mixed sequence oligonucleotide, MIX24. “HER2-1”=HER2-1-treatedcells. “HER2-205”=HER2-205-treated cells. FIG. 2A: Representative imagesof neutral comet assays performed 24 h after HER2-205 treatment in MCF7and BT474 cells. FIG. 2B: a chart showing the quantification oftriplex-induced DNA double strand breaks using the neutral comet assayas measured by tail moment in multiple breast cancer cell lines. FIG.2C: a chart showing that triplex-induced DNA damage increases in celllines containing multiple copies of the HER2 gene. FIG. 2D: a chartshowing the frequency of cells with more than 5 γH2AX foci per nucleifollowing 24 h HER2-205 treatment. FIG. 2E: Representative images ofHER2-205 induced 53BP1 (green) and γH2AX (red) foci in nuclei (blue)compared to MIX24 24 h post-treatment in BT474 cells. FIG. 2F: a chartshowing the analysis of triplex-induced apoptosis as measured byAnnexin-V staining in breast cancer cell lines 24 h post TFO-treatment.FIG. 2G: a chart showing that the level of triplex-induced apoptosisincreases with gene copy number. FIG. 2H: a chart showing the analysisof triplex-induced apoptosis in HER2-positive ovarian cancer cells asmeasured by Annexin V staining 48 h post-treatment. **** denotesp<0.0001, *** denotes p<0.001, ** denotes p<0.01, and * denotes p<0.05

FIGS. 3A-3I include diagrams showing triplex-induced DNA damage andactivation of apoptosis in several HER2-positive breast and ovariancancer cell lines. “UT”=untreated cells. “Mock”=cells with transfectionreagent only. “MIX24”=cells treated with control mixed sequenceoligonucleotide, MIX24. “HER2-1”=HER2-1-treated cells.“HER2-205”=HER2-205-treated cells. FIG. 3A: a chart showing thequantification of cells with more than 5 γH2AX and/or 53BP1 foci pernuclei in BT474 cells treated with HER2-205 or MIX24. FIG. 3B: imagesshowing that triplex formation induces apoptosis in HER2-positive breastcancer cell lines as measured by Western blot analysis of cleaved PARP.FIG. 3C: images showing the detection of HER2 copies in interphasenuclei by dual color FISH with HER2 probe (red) and chromosome 17 probe(green). FIG. 3D: images showing the immunofluorescence of γH2AX in PE01ovarian cancer cells 24 h post-treatment with HER2-205 or MIX24. FIG.3E: representative immunofluorescence images of γH2AX foci in SKOV3ovarian cancer cells 24 h following treatment with HER2-205 or MIX24.FIG. 3F: a chart showing the frequency of PEO1 and SKOV3 cells positivefor γH2AX following 24 h treatment. FIG. 3G: a chart showing thequantification of triplex-induced DNA double strand breaks using theneutral comet assay as measured by tail moment. FIG. 3H: images showinga monolayer growth assay that demonstrates a decrease in cell survivalin PEO1 and SKOV3 cells treated with HER2-205 72 h after treatment. FIG.3I: images showing a western blot analysis of activation of apoptosis asmeasured by cleaved PARP in ovarian cancer cells following TFOtreatment.

FIGS. 4A-4G include diagrams showing the in vivo effect of HER2-205 onhuman HER2-positive cancer xenografts. Tumor growth delay curves ofBT474 xenografts generated by subcutaneous injection of female athymicnude mice. Twenty-eight days after implantation mice were treated byintraperitoneal (IP) injection with three doses of (FIG. 4A) HER2-205,(FIG. 4B) trastuzumab and (FIG. 4C) MIX24 at a concentration of 20mg/kg. Arrow indicates administration of first dose. Tumor growthmeasurements ±SEM are shown. FIG. 4D: a Kaplan-Meier plot of thepercentage of tumors smaller than three times baseline size. Baselinesize was defined as tumor size on the first day of treatment [Day 28 in(FIG. 4A) and Day 21 in (FIG. 4B) and (FIG. 4C)]. FIG. 4E: imagesshowing a histopathologic analysis of BT474 tumor sections from mice 24h after treatment with a single dose of HER2-205 (20 mg/kg body weight)or vehicle. Haematoxylin and eosin (H&E), caspase 3, HER2, Ki67 stain at4× magnification. Scale bar=10 μm. FIG. 4F: an image showing a highermagnification of H&E tumor section from HER2-205 treatment specimen.FIG. 4G: a Kaplan-Meier plot of the percentage of SKOV3 ovarian cancertumors smaller than three times baseline size. Mice were treated with 3doses of HER2-205 at a concentration of 20 mg/kg or cisplatin at aconcentration of 10 mg/kg.

FIGS. 5A-5F include diagrams showing the molecular mechanism ofanticancer activity. “UT”=untreated cells. “Mock”=cells withtransfection reagent only. “MIX24”=cells treated with control mixedsequence oligonucleotide, MIX24. “HER2-205”=HER2-205-treated cells. FIG.5A: images showing a western blot analysis of the phosphorylation statusof the DNA damage response proteins Chk1 and Chk2 following TFOtreatment. FIG. 5B: images showing that the knockdown of the NER factor,XPD, in BT474 cells results in a decrease in the induction of apoptosisas measured by cleaved PARP and pH2AX Y142. pH2AX Y142 is an essentialpost-translational modification for the recruitment of pro-apoptoticfactors to the tail of γH2AX. FIG. 5C: images showing that HER2-205activates p53-independent apoptosis in HER2-positive BT474 cells. FIG.5D: a chart showing the analysis of HER2 gene expression by RT-PCR andFIG. 5E: images showing that determination of HER2 protein levels andphosphorylation status using Western blot analysis provide evidence thatHER2-205 achieves therapeutic activity using a mechanism that isindependent of HER2 cellular function. FIG. 5F: a schematic illustrationof molecular mechanism of gene-targeted apoptosis. TFO binding in themajor groove of duplex DNA causes a distortion of the double helix,which can induce DNA replication fork collapse and induction of DNAdouble strand breaks (DSBs). DNA damage response activates anXPD-dependent but p53-independent apoptotic pathway.

FIGS. 6A-6D include diagrams that support a molecular mechanism that isindependent of HER2 signaling pathways. “UT”=untreated cells.“Mock”=cells with transfection reagent only. “MIX24”=cells treated withcontrol mixed sequence oligonucleotide, MIX24.“HER2-205”=HER2-205-treated cells. FIG. 6A: a chart showing thequantification of phosphorylated ATM by flow cytometry followingtreatment with HER2-205. Western blot analysis of the phosphorylationstatus of HER family receptors (FIG. 6B) HER3, (FIG. 6C) HER4, and (FIG.6D) EGFR (HER1) in multiple breast cancer cell lines following HER2-205treatment.

FIG. 7 includes a schematic illustration showing TFOs that are designedto bind to polypurine sites in non-coding regions of the HER2 gene,which is located on chromosome 17. Two TFOs, HER2-5922-2 and HER2-40118,were designed to target the introns of the HER2 gene.

FIGS. 8A-8B include charts showing that TFOs targeting non-codingregions can also induce DSBs and apoptosis. FIG. 8A includes a chartshowing TFOs targeting non-coding regions of the HER2 gene can induceDNA DSBs. The chart shows quantification of triplex-induced DSBs usingthe neutral comet assay as measured by tail moment. Triplex-induced DNAdamage was assessed 24 hours post treatment. FIG. 8B includes a chartshowing that TFOs targeting non-coding regions of the HER2 gene caninduce apoptosis. The chart shows analysis of triplex-induced apoptosisas measured by Annexin-V staining 24 hours post-treatment in BT474cells. **** denotes p<0.0001, *** denotes p<0.001, ** denotes p<0.01,and * denotes p<0.05.

DETAILED DESCRIPTION

Described herein is a method of reducing, in a population of cells, thenumber of p53-depleted cancer cells in which a HER2 gene is amplifiedand agents useful to reduce the number of p53-depleted cancer cellscomprising an amplified HER2 gene. In specific embodiments, the agentsare triplex-forming oligonucleotides (TFOs) that are targeted to apolypurine site in an amplified HER2 gene in p53-depleted cancer cells.

In one embodiment, the method comprises contacting a population ofcells, such as tissue, comprising p53-depleted cancer cells in which aHER2 gene is amplified with triplex forming oligonucleotides (TFOs)targeted to a polypurine target site in the HER2 gene(s), underconditions under which the TFOs enter the p53-depleted cancer cells insufficient quantity to induce apoptosis.

Advancements in DNA sequencing technology have not only revealedcommonly mutated and deleted genes across cancer types, but also enabledidentification of amplified cancer-promoting genes⁸. These amplifiedgenes include epigenetic regulators, cell cycle-associated genes, andgenes linked to signaling pathways, such as the EGFR and HER2 genes⁹.Described herein is an approach for targeted therapeutics that can beused in the treatment of p53-depleted cancers characterized by geneamplification and that has limited toxicity to normal tissue. Thelimited toxicity is at least due to the localized effect and targetingof the TFOs to cells that have HER2-amplified genes and thus are likelyto be the cancerous cells in the tissue. Described herein are agents andmethods demonstrating that manipulation of DNA damage response is aseffective in its anticancer activity as targeting the individualoverexpressed protein product.

Provided herein are triplex-forming oligonucleotides (TFOs, alsoreferred to as triplex-inducing oligonucleotides) for the induction ofp53-independent apoptosis. TFOs are molecules that function assequence-specific gene targeting/modification tools. Without wishing tobe bound by theory, it has been shown that the TFOs bind to the majorgroove of duplex DNA and are restricted to sites with purines (alsoreferred to as polypurine sites) on one strand and pyrimidines on theother.

HER2 Gene Amplification and NER-Dependent Repair

Gene amplification is observed in a broad spectrum of cancers,contributing not only to incipient cancer development, but also to thedevelopment of drug resistance. HER2 gene amplification (amplificationof human epidermal growth factor receptor 2-encoding gene) is observedin a vast majority of cancers. Cancers with HER2 gene amplification orover-expression of the HER2 protein are sometimes referred to asHER2-positive cancers. Non-limiting examples of such cancers includebreast cancer, ovarian cancer, colorectal cancer, gastric cancer, lungcancer, and endometrial cancer. HER2 gene amplification has beenidentified in about 25% of breast cancers.

Disclosed herein are TFOs targeted to specific regions of the HER2 gene.These TFOs can be utilized for a p53-independent cancer therapy. Thereare several polypurine sites in the HER2 gene that are susceptible totriplex formation. Binding of TFOs to the HER2 gene (e.g., major grooveregions on the HER2 gene) causes DNA perturbation that can impedereplication fork progression, resulting in fork collapse and helixdistorting structures (e.g., lesions or, more specifically, DNA doublestrand breaks (DSBs))¹⁴. Under normal circumstances (e.g., low HER2 genecopy levels), these helix distorting structures trigger the nucleotideexcision repair (NER) pathway, which repairs the helix distortingstructures. This ability of the NER pathway to resolve low levels oftriplex-induced DNA damage allows normal cells to tolerate the formationof a few triplexes^(16,17). In contrast, if there is HER2 geneamplification and consequently high levels of triplex formation,NER-dependent DNA repair is ineffective and instead apoptosis istriggered¹⁵. HER2 gene amplification in cancers, such as breast cancers,provides an opportunity to test the efficacy of TFOs as anapoptosis-inducing agent in cancer cells, but not in healthy cells,which lack HER2 amplification¹⁸ (FIGS. 1A-1C).

XPD, a transcription factor II H (TFIIH) subunit, plays a key role inthis NER pathway by operating as a 5′-3′ helicase to unzip the DNA. Ininstances of high DNA damage (or high triplex formation), XPD isrequired for p53-mediated apoptosis (see U.S. Pat. No. 9,587,238, therelevant disclosures of which are herein incorporated as reference).Previous studies established that in cases of excess DNA damage, anapoptotic pathway is initiated that is dependent on the presence of bothXPD and p53. This, in part, explains the chemotherapeutic drugresistance and the difficulty in treating p53-defective conditions.

P53 Tumor Supressor

Disclosed herein are methods and compositions for inducing apoptosis inp53-depleted cells comprising an amplified HER2 gene. P53 (also referredto as TP53 or p53 tumor suppressor) is a gene on the 17^(th) chromosome(17p13.1) that encodes p53 protein (also referred to as TP53 or tumorprotein). The protein is a regulator in the cell cycle and plays therole of a tumor suppressor. The p53 tumor suppressor regulatespro-apoptotic pathways in response to severe DNA damage. Under normal,non-pathological conditions, p53 expression is low. DNA damage andrelated signals upregulate its expression to initiate growth arrest, DNArepair, and, in extreme cases, apoptosis. Typically, growth arrestinhibits replication of damaged DNA; however, in cancerous cells this isbypassed. As explained herein, gene amplification manifests in cancerouscells and can result in ineffective DNA repair (for example, ineffectiveNER-mediated DNA repair). In such cases, p53 is relied on for apoptosisof the damaged cells.

Mutations in p53 are correlated with a broad spectrum of aggressivecancers and have been implicated in as many as 50% of all human tumors,highlighting the importance of this gene and the impact of ap53-independent chemotherapeutic approach. Over 50% of human cancersexhibit chemotherapeutic resistant phenotypes due to loss of functionp53 mutations, which lead to an inability to trigger apoptosis. Previousstudies attempted to address cancer treatment in p53-defectiveconditions by upregulating wild-type p53 or augmenting the activity ofwild-type p53 (Smith and Seo, Mutagenesis 17(2), 149-156, 2002).Additional strategies to overcome this challenge include attempts tomodify the p53 gene through gene editing, reactivate p53 genes withchemotherapeutic drugs, or suppress p53 mutant aggregation. Thesestrategies have had limited success.

The term “p53-depleted” refers to cells, such as cancer cells, in whichp53 is reduced, lacking or mutated. In some embodiments, a p53-depletedcancer cell is a cell that does not express p53. It can also refer tosignificantly decreased p53 expression under conditions under which p53is typically upregulated (e.g., in response to a DNA lesion). Mutationsin p53 have been shown to give rise to different isoforms, some of whichgive rise to tissue-specific cancers. The term “p53-depleted” alsoincludes cells, such as cancer cells, in which the p53 gene has amutation (e.g., loss of function mutation, gain of function mutation,etc.) and produces a protein that is dysfunctional (e.g., displays no orreduced function). This may also occur through the production of atruncated p53 protein that is dysfunctional. Most p53 mutations aremissense mutations. In some embodiments, the p53-mutated cell is ahomozygote mutant. In some embodiments, the p53-mutant cell is aheterozygote, carrying a wild-type p53 allele and a mutant p53 allele.Previous studies have shown that in some heterozygote cases, the mutantallele functions in a dominant negative manner, suppressing theexpression of the wild-type allele. Loss of wild-type p53 and p53mutations have been shown to occur in both early and late tumorigenesis.Some p53 mutations, referred to as gain-of-function p53 mutations,result in p53 mutant proteins that have additional oncogenic propertiesand promote cancer progression (Rivlin et al., Genes & Cancer2(4):466-474, 2011).

Triplex Forming Oligonucleotides (TFOs)

Triplex-forming oligonucleotides (TFOs) form triplexes, which are DNAstructures comprised of an additional RNA or DNA binding sequence.Without wishing to be bound by theory, they are believed to bind in themajor groove of duplex DNA. Purine motif TFOs (comprised of G and A)form G*G:C and A*A:T triplets and bind in antiparallel orientation, viareverse Hoogsteen base pairing, with regard to the purine strand of theduplex. In contrast, pyrimidine motif TFOs (C/T) form triplexes inparallel orientation, via forward Hoogsteen alignment, and form C⁺*G:Cand T*A:T triplets. Mixed purine and pyrimidine TFOs bind in eitherparallel or antiparallel orientation and form G*G:C and T*A:T triplets.(Maldonado, R., et al. RNA 24(3): 371-380, 2018 and Basye, J., et al.Nucleic acids research 29(23): 4873-4880, 2001).

Applications of HER2 Targeted TFOs

As described, HER2-targeted TFOs trigger an alternative pathway, ap53-independent apoptotic pathway. HER2-targeted TFOs induce copy numberdependent DNA double strand breaks (DSBs) and activate apoptosis in HER2gene amplified cancer cells and human tumor xenografts via a mechanismthat is independent of HER2 cellular function as well as independent ofp53. In specific embodiments, HER2-targeted TFOs, HER2-1 (SEQ ID NO:3),HER2-205 (SEQ ID NO:4), HER2-5922-2 (SEQ ID NO:7), and HER2-40118 (SEQID NO: 8), trigger p53-independent apoptosis in cancer cells comprisingamplified HER2 gene.

In some embodiments, the HER2-targeted TFOs target polypurine targetsites in the promoter region of the HER2 gene (e.g., the HER2-1 TFO (SEQID NO: 3)). In some embodiments, the HER2-targeted TFOs targetpolypurine target sites in the coding region of the HER2 gene (e.g., theHER2-205 TFO (SEQ ID NO: 4)). In some embodiments, the HER2-targetedTFOs target introns or non-coding regions of the HER2 gene. For example,the HER2-5922-2 TFO (SEQ ID NO: 7) targets a site within intron 2 of theHER 2 gene, and the HER2-40118 (SEQ ID NO: 8) TFO targets intron 19 ofthe HER2 gene.

Disclosed herein is a method of reducing, in a population of cells, thenumber of p53-depleted cancer cells comprising an amplified HER2 gene.As described, this method can be carried out in a population of cells,such as in a tissue or organ. As used herein, the term “reducing” refersto decreasing the number of living cells by inducing apoptosis in thecells. The reduction could decelerate rapid cell growth or deceleratehyperplasia, which are two common characteristics of cancerous cells.

The methods disclosed herein includes contacting p53-depleted cancercells comprising amplified HER2 gene with triplex-formingoligonucleotides (TFOs) targeted to a polypurine target site in theamplified-HER2 gene.

In some embodiments, the TFOs are polypurine TFOs. Polypurine TFOs arerich in adenine and/or guanine bases, and, without wishing to be boundby theory, are believed to bind to the major groove of their polypurinetarget sites in an antiparallel fashion. As used, the term “polypurineTFO” refers to purine motif TFOs or TFOs rich in purines (adenine and/orguanine bases). As used, the term “polypurine target site” refers to aDNA duplex having a strand rich in purines (adenine and/or guaninebases). The terms “polypurine target strand” and “polypurine strand”refer to the strand in the polypurine target site that is rich inpurines (adenine. guanine or both adenine and guanine bases). In someembodiments, a sequence is referred to as “rich in purines” when 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more of itsnucleotides have adenine and/or guanine bases.

An example of a polypurine target site identified in the promoter regionof the HER2 gene is a DNA duplex having the sequence5′-AGGAGAAGGAGGAGGTGGAGGAGGAGGG-3′ (SEQ ID NO:1) bound to5′-CCCTCCTCCTCCACCTCCTCCTTCTCCT-3′ (SEQ ID NO:10). Another example of apolypurine target site identified in the coding region of the HER2 geneis a DNA duplex having the sequence 3′-CCCCGAGGAGGAGCGGGAGAACGGGGGG-5′(SEQ ID NO:2) bound to 5′-GGGGCTCCTCCTCGCCCTCTTGCCCCCC-3′ (SEQ IDNO:11). (FIG. 1B).

Another example of a polypurine target site identified in the non-codingregion of the HER2 gene is a DNA duplex having the sequence3′-GGGAAAGAGGAGGGGGTGAGAGGAGTGGGG -5′ (SEQ ID NO: 5) bound to5′-CCCTTTCTCCTCCCCCACTCTCCTCACCCC-3′ (SEQ ID NO: 12). Another example ofa polypurine target site identified in the non-coding region of the HER2gene is a DNA duplex having the sequence 3′-GGGGGAAACAGGGAGGGTGGGG-5′(SEQ ID NO: 6) bound to 5′-CCCCCTTTGTCCCTCCCACCCC-3′ (SEQ ID NO: 13).(FIG. 7).

Formation of the triplex after introduction of a TFO occurs via reverseHoogsteen hydrogen bonds between the third strand (TFO) and thepolypurine strand of the duplex

In some embodiments, a TFO has a nucleotide sequence that iscomplementary to SEQ ID NOs: 10, 11, 12 and 13 and/or binds to at least13 nucleotides in a polypurine target strand, such as at least 13nucleotides in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO: 5 or SEQ ID NO: 6.In some embodiments, a TFO binds to 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in a polypurine targetstrand. TFOs can bind to contiguous or non-contiguous nucleotides in apolypurine target site. The TFOs described herein can be any TFOsequence that is targeted to a polypurine target site in a HER2 gene,for example, polypurine target sites SEQ ID NO:1, SEQ ID NO:2, SEQ IDNO: 5 or SEQ ID NO: 6. In some embodiments, the TFOs are at least 13nucleotides in length. In some embodiments, the TFOs range from 13 to 30nucleotides in length. For example, the TFOs can be 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides inlength. In further embodiments, the TFOs are shorter (e.g., 8, 9, 10,11, or 12 nucleotides).

Examples of HER2-targeted TFOs are HER2-1(5′-GGGAGGAGGAGGTGGAGGAGGAAGAGGA-3′; SEQ ID NO:3), HER2-205(5′-GAGGAGGAGTGGGAGAATGGGGGG-3′; SEQ ID NO:4), HER2-5922-2(5′-GGGAAAGAGGAGGGGGTGAGAGGAGTGGGG-3′; SEQ ID NO: 7), and HER2-40118(5′-GGGGGAAATAGGGAGGGTGGGG-3′; SEQ ID NO: 8). HER2-1 hybridizes to SEQID NO:1, under physiological conditions. HER2-205 hybridizes to SEQ IDNO:2, under physiological conditions. HER2-5922-2 hybridizes to SEQ IDNO: 5, under physiological conditions. HER2-40118 hybridizes to SEQ IDNO: 6, under physiological conditions (FIGS. 1D and 7).

As used, the term “complementary” refers to the capacity for precisepairing (also referred to as hybridization) between two nucleotides. Forexample, if a nucleotide at a certain position of an oligonucleotide iscapable of hydrogen bonding with a nucleotide at a correspondingposition of a target RNA, then the nucleotide of the oligonucleotide andthe nucleotide of the target RNA are complementary to each other at thatposition. As understood by one of ordinary skill in the art, forcomplementary base pairings, adenosine-type bases (A) are complementaryto thymidine-type bases (T) or uracil-type bases (U), cytosine-typebases (C) are complementary to guanosine-type bases (G), and universalbases such as 3-nitropyrrole or 5-nitroindole can hybridize to and areconsidered complementary to any A, C, U, or T. In some embodiments, themethods and agents of the present disclosure can include Inosine (I).Inosine has also been considered in the art to be a universal base andis considered complementary to A, C, U or T.

In some embodiments, the TFO is a nucleotide sequence that is at least90% identical to SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 7 or SEQ ID NO: 8.As used herein, the term “identity” or “identical” refers to sequenceidentity, which refers to two nucleotides being identical. In someembodiments, the TFO is a nucleotide at least 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99% or 100% identical to SEQ ID NO:3, SEQ ID NO:4,SEQ ID NO: 7 or SEQ ID NO: 8.

The sequence on a HER2 gene to which a TFO is targeted is referred to asa “target sequence.” For example, a TFO that is targeted to a polypurinesite is one that hybridizes to that polypurine site under physiologicalconditions, such as in the case of in vivo administration or treatment.“Targeted” can also refer to a TFO that specifically hybridizes to apolypurine site (partially or completely). For example, the TFOhybridizes to a sequence in the target sequence or target sequence, butdoes not hybridize to any other (off-target) nucleotide sequence withinthe cell and would not hybridize to a sequence within a cell that lacksthe polypurine site, under physiological conditions.

In the methods of the present disclosure, TFOs are contacted withp53-depleted cells that comprise amplified HER2 gene by a variety ofapproaches, such as by administering TFOs to an individual in need of areduction in a population of p53-deficient cells that comprise amplifiedHER2 gene. For example, TFOs in an appropriate delivery vehicle can beadministered to an individual with cancer in which cancer cells are p53depleted and comprise amplified HER2 gene. The TFOs are contacted withsuch cells by any manner and under conditions that result in entry intocells in the individual. For example, TFOs can be introduced into anindividual by injection, infusion, or any delivery method, such as thosedescribed further below.

In some embodiments of the present disclosure, the TFOs are administeredto an individual who has been screened for a p53 mutation, hasHER2-positive cancer cells, and thus has been identified as a candidatefor this p53-independent TFO-treatment. Non-limiting examples of methodsfor identifying an individual with p53 mutations include genetic testingof the DNA found in sera or other body fluids (see Rivlin et al., Genes& Cancer 2(4):466-474, 2011, the relevant disclosures of which areherein incorporated as reference).

In some embodiments, the methods of the present disclosure are for thetreatment of p53-mutated cancers. Non-limiting examples of suchp53-mutated cancers include breast cancer, ovarian cancer, renalcarcinoma, lung cancer, colon carcinoma, hepatocellular carcinoma,prostate cancer, bladder cancer, and pancreatic neoplasia. The methodsof the present disclosure can include administering the TFOs herein tothe cells of the aforementioned cancers (e.g., breast cancer cells,ovarian cancer cells, renal cell carcinoma cells, lung cancer cells,colon cancer cells, colorectal cancer cells, gastric cancer cells, andendometrial cancer cells).

Li-Fraumeni Syndrome Application

In some embodiments, the present disclosure includes methods andcompositions for the treatment of an individual with Li-FraumeniSyndrome (LFS) or treatment of a cancer in an individual with LFS. LFSis a cancer predisposition syndrome characterized by germline mutationsof p53 (Smith and Seo, Mutagenesis 17(2), 149-156, 2002). Individualswith LFS are susceptible to a broad spectrum of cancers and aresusceptible to early onset of these cancers. Of the spectrum ofLi-Fraumeni-associated tumors, breast cancer, sarcomas of the softtissues and bone, acute leukemias, and brain tumors are among the mostcommon (Nichols et al., Cancer Epidemiology and Prevention Biomarkers10(2): 83-87, 2001, the relevant disclosures of which are hereinincorporated by reference). The lifetime risk of an LFS patient todevelop cancer has been estimated to be as high as 90%. Non-limitingexamples of types of cancer commonly found in families with LFS includeosteosarcoma (bone cancer), soft-tissue sarcoma, acute leukemia, breastcancer, brain cancer, adrenal cortical tumors, and acute leukemia.

In some embodiments, an individual is screened for HER2 geneamplification before administration of the TFO. Methods for detection ofgene amplification are known in the art. Non limiting examples of thesemethods include conventional cytogenetics, Southern blotting,quantitative PCR, fluorescence in situ hybridization (FISH), comparativegenomic hybridization (CGH), and microarray technology.

Due to the limited toxicity associated with the described TFOs, inalternative embodiments, a TFO targeted to at least one sequence in HER2gene can be administered to an individual diagnosed with cancer toinduce p53 independent apoptosis in p53-depleted cells comprising anamplified HER2 gene prior to or without screening for HER2 geneamplification.

Chemical Modifications to TFOs

In some embodiments, the TFOs have backbone modifications. Unmodifiedpurine TFOs bind well under physiologic conditions, but bindingefficiency can sometimes be inhibited at physiologic K⁺ conditions.Backbone modifications can augment the binding efficiency of such TFOs.Various modifications for purine TFOs are disclosed in Knauert andGlazer, Human Molecular Genetics 10(20): 2243-2251, 2001, the relevantdisclosures of which are herein incorporated by reference. Non-limitingexamples of backbone modifications to the TFOs includephosphorothioates, phosphorodithioates, methylphosphonates,phosphoramidates, boranophosphate oligos, polyamides, methylene(methylimino) linkages, morpholino oligos, and combinations thereof.TFOs with polyamide backbone modifications bind to the minor groove ofthe DNA duplex, rather than the major groove.

Combination Therapies

Disclosed herein are methods of administering TFOs in sufficientquantity to induce p53-independent apoptosis in p53-depleted cellscomprising an amplified HER2 gene. In some embodiments, one type of TFO(e.g., either HER2-1 or HER2-205) is administered. In some embodiments,TFOs of more than one type are administered (e.g., a mixture of TFOs, amixture of HER2-1 and HER2-205, etc.). Herein, reference to“administering TFOs” can also refer to the administration of TFOs ofmore than one type.

In some embodiments, the one type of TFO is administered in combinationwith at least one non-TFO (e.g., a non-TFO anticancer agent). In someembodiments, more than one type of TFO is administered with at least onenon-TFO (e.g., a non-TFO anticancer agent). An anticancer agent that isnot a TFO can be, for example, a protein, a nucleic acid, a smallmolecule, or a drug for the treatment of cancer. This anticancer agentcan have any anti-cancer effect on the population of cells that it isadministered to including, but not limited to, a cytotoxic, apoptotic,anti-mitotic anti-angiogenesis or inhibition of metastasis effect. Thisanticancer agent can also affect DNA damage response (e.g., a DNA repairinhibitor). In some embodiments, the second anticancer agent is a drugdirected against overexpressed protein products.

Anticancer agents include, for example, antimetabolites, inhibitors oftopoisomerase I and II, alkylating agents and microtubule inhibitors(e.g., taxol). Non-limiting examples of anticancer agents includeadriamycin aldesleukin; alemtuzumab; alitretinoin; allopurinol;altretamine; amifostine; anastrozole; arsenic trioxide; Asparaginase;BCG Live; bexarotene capsules; bexarotene gel; bleomycin; busulfanintravenous; busulfan oral; calusterone; capecitabine; carboplatin;carmustine; carmustine with Polifeprosan 20 Implant; celecoxib;chlorambucil; cisplatin; cladribine; cyclophosphamide; cytarabine;cytarabine liposomal; dacarbazine; dactinomycin; actinomycin D;Darbepoetin alfa; daunorubicin liposomal; daunorubicin, daunomycin;Denileukin diftitox, dexrazoxane; docetaxel; doxorubicin; doxorubicinliposomal; Dromostanolone propionate; Elliott's B Solution; epirubicin;Epoetin alfa estramustine; etoposide phosphate; etoposide (VP-16);exemestane; Filgrastim; floxuridine (intraarterial); fludarabine;fluorouracil (5-FU); fulvestrant; gemcitabine, gemtuzumab ozogamicin;goserelin acetate; hydroxyurea; Ibritumomab Tiuxetan; idarubicin;ifosfamide; imatinib mesylate; Interferon alfa-2a; Interferon alfa-2b;irinotecan; letrozole; leucovorin; levamisole; lomustine (CCNU);meclorethamine (nitrogen mustard); megestrol acetate; melphalan (L-PAM);mercaptopurine (6-MP); mesna; methotrexate; methoxsalen; mitomycin C;mitotane; mitoxantrone; nandrolone phenpropionate; Nofetumomab; LOddC;Oprelvekin; oxaliplatin; paclitaxel; pamidronate; pegademase;Pegaspargase; Pegfilgrastim; pentostatin; pipobroman; plicamycin;mithramycin; porfimer sodium; procarbazine; quinacrine; Rasburicase;Rituximab; Sargramostim; streptozocin; talbuvidine (LDT); talc;tamoxifen; temozolomide; teniposide (VM-26); testolactone; thioguanine(6-TG); thiotepa; topotecan; toremifene; Tositumomab; Trastuzumab;tretinoin (ATRA); uracil mustard; valrubicin; valtorcitabine (monovalLDC); vinblastine; vinorelbine; zoledronate; and mixtures thereof, amongothers (see U.S. Pat. No. 9,643,922, the relevant disclosures of whichare herein incorporated by reference).

Non-limiting examples of anticancer agents include oestrogen receptormodulators, androgen receptor modulators, retinoid receptor modulators,cytotoxic agents, antiproliferative agents, prenyl-protein transferaseinhibitors, HMG-CoA reductase inhibitors, reverse transcriptaseinhibitors and further angiogenesis inhibitors.

Non-limiting examples of retinoid receptor modulators includebexarotene, tretinoin, 13-cis-retinoic acid, 9-cis-retinoic acid,.alpha.-difluoromethylornithine, ILX23-7553,trans-N-(4′-hydroxyphenyl)retinamide and N-4-carboxyphenylretinamide(see U.S. Pat. No. 10,093,623, the relevant disclosures of which areherein incorporated by reference).

Non-limiting examples of cytotoxic agents include tirapazimine,sertenef, cachectin, ifosfamide, tasonermin, lonidamine, carboplatin,altretamine, prednimustine, dibromodulcitol, ranimustine, fotemustine,nedaplatin, oxaliplatin, temozolomide, heptaplatin, estramustine,improsulfan tosylate, trofosfamide, nimustine, dibrospidium chloride,pumitepa, lobaplatin, satraplatin, profiromycin, cisplatin, irofulven,dexifosfamide, cis-aminedichloro(2-methylpyridine)platinum,benzylguanine, glufosfamide, GPX100,(trans,trans,trans)bis-mu-(hexane-1,6-diamine)-mu-[diamineplatinum(II)]bi-s[diamine(chloro)platinum(II)]tetrachloride,diarisidinylspermine, arsenic trioxide,1-(11-dodecylamino-10-hydroxyundecyl)-3,7-dimethylxanthine, zorubicin,idarubicin, daunorubicin, bisantrene, mitoxantrone, pirarubicin,pinafide, valrubicin, amrubicin, antineoplaston,3′-deamino-3′-morpholino-13-deoxo-10-hydroxycarminomycin, annamycin,galarubicin, elinafide, MEN10755 and4-demethoxy-3-deamino-3-aziridinyl-4-methylsulfonyldaunorubicin (see WO00/50032, the relevant disclosures of which are herein incorporated byreference).

Non-limiting examples of antiproliferative agents include antisense RNAand DNA oligonucleotides such as G3139, ODN698, RVASKRAS, GEM231 andINX3001 and antimetabolites such as enocitabine, carmofur, tegafur,pentostatin, doxifluridine, trimetrexate, fludarabine, capecitabine,galocitabine, cytarabine ocfosfate, fosteabine sodium hydrate,raltitrexed, paltitrexid, emitefur, tiazofurin, decitabine, nolatrexed,pemetrexed, nelzarabine, 2′-deoxy-2′-methylidenecytidine,2′-fluoromethylene-2′-deoxycytidine,N-[5-(2,3-dihydrobenzofuryl)sulfonyl]-N′-(3,4-dichlorophenyl)urea,N6-[4-deoxy-4-[N2-[2(E),4(E)-tetradecadienoyl]-glycylamino]-L-glycero-B-L-mannoheptopyranosyl]adenine,aplidine, ecteinascidin, troxacitabine,4-[2-amino-4-oxo-4,6,7,8-tetrahydro-3H-pyrimidino[5,4-b]-1,4-thiazin-6-yl-(S)ethyl]-2,5-thienoyl-L-glutamicacid, aminopterin, 5-fluorouracil, alanosine,11-acetyl-8-(carbamoyloxymethyl)-4-formyl-6-methoxy-14-oxa-1,11-diazatetr-acyclo(7.4.1.0.0)tetradeca-2,4,6-trien-9-ylaceticacid ester, swainsonine, lometrexol, dexrazoxane, methioninase,2′-cyano-2′-deoxy-N4-palmitoyl-1-B-D-arabinofuranosyl cytosine and3-aminopyridine-2-carboxaldehyde thiosemicarbazone. “Antiproliferativeagents” also include monoclonal antibodies to growth factors other thanthose listed under “angiogenesis inhibitors”, such as trastuzumab (forexamples, see U.S. Pat. No. 6,069,134, the relevant disclosures of whichare herein incorporated by reference).

The first drugs directed against overexpressed protein products weremajor breakthroughs in cancer therapeutics. For example, trastuzumab(HERCEPTIN®) targets the HER2 receptor tyrosine kinase, which isoverexpressed in about 25% of breast tumors due to gene amplification¹⁰.Trastuzumab works, at least in part, by disrupting HER2 signaling, whichresults in cell cycle arrest and suppression of cell growth andproliferation¹¹. While trastuzumab has proven to be effective inprolonging the survival of HER2-positive breast cancer patients, primaryand acquired drug resistance limits overall success rates. Similarproblems hamper the long-term efficacy of other cancer drugs, includingthe tyrosine kinase inhibitors gefitinib (IRESSA®) and erlotinib(TARCEVA®), which target EGFR gene amplification in breast, colorectal,and lung cancer^(12,13).

Methods of Administering TFOs

The TFOs of the present disclosure may be administered to an individualby any route or in any delivery vehicle.

In some embodiments, the TFOs are administered in a delivery vehicle(e.g., lipid-based nanoparticles). The TFOs can be conjugated to thelipid-based nanoparticles. Alternatively, the TFOs can be encapsulatedin the lipid-based nanoparticles. One example of lipid-basednanoparticles is lipid nanoparticles that contain a solid lipid corematrix with the ability to solubilize lipophilic molecules. The term“solid” refers to a nanoparticle that is solid at room temperature andatmospheric pressure. The lipid nanoparticles can have a nanostructurecore (solid or hollow) and a lipid layer. The diameter of the core canbe less than or equal to about 500 nm, less than or equal to about 250nm, less than or equal to about 100 nm, less than or equal to about 75nm, less than or equal to about 50 nm, less than or equal to about 40nm, less than or equal to about 35 nm, less than or equal to about 30nm, less than or equal to about 25 nm, less than or equal to about 20nm, less than or equal to about 15 nm, or less than or equal to about 5nm. In some embodiments, the core is less than 1000 nm. In someembodiments, the core is 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm,9 nm, 10 nm, 20 nm, 30 nm, 40 nm 50 nm, 60 nm, 70 nm, 80 nm, 90 nm, 100nm, 120 nm, 140 nm, 160 nm, 180 nm, 200 nm, 220 nm, 240 nm, 260 nm, 280nm, 300 nm, 320 nm, 340 nm, 360 nm, 380 nm, 400 nm, 420 nm, 440 nm, 460nm, 480 nm, or 500 nm in diameter.

The lipid nanoparticle can be a solid lipid nanoparticle or a polymericnanoparticle. Methods for making solid liquid nanoparticles arewell-established in the art (see, for example, Gasco, M. R.,Nanoparticelle Lipidiche Solide Quali Sistemi Terapeutici Colloidali,NCF nr. 7: 71-73, 1996; Kozariara et al., Pharmaceutical Research,20(11): 1772, 2003; and Lockman et al., Journal of Controlled Release,93:271-282, 2003, the relevant disclosures of which are hereinincorporated by reference).

In a polymeric lipid nanoparticle the polymer can be any ionic orionizable polymer or copolymer known to those of skill in the artincluding polymers and copolymers of, for example, polyglycine,polyethylene glycol, heparin, hydroxypropylmethylcellulose,hydroxyethylcellulose, hydroxypropylcellulose, polyvinylpyrrolidone,polyvinyl alcohol, poly-beta amino esters (PBAEs), methacrylic acidcopolymers, ethyl acrylate-methyl methacrylate copolymers, and mixturesthereof. In some embodiments, the first functionalized polymer can bepoly(glycolic acid), poly(lactic acid) (PLA), or copolymers thereof,such as poly(D,L-lactide-co-glycolide), or mixtures thereof.

In some embodiments, the TFOs are delivered usingpoly(lactic-co-glycolic acid) (PLGA) nanoparticles or PLA nanoparticles.In some embodiments, the PLGA nanoparticles or PLA nanoparticles areloaded with the TFOs of the present disclosure. In some embodiments thenanoparticles include an agent conjugated to their surface, such aspolyethylene glycol (PEG) and hyperbranched polyglycerols (HPG).

In some embodiments, the lipid nanoparticles include cationic lipids oranionic lipids. Alternatively, the lipid nanoparticles can includeneutral lipids. Non-limiting examples of cationic lipids include3β-(N-(N′,N′-dimethylaminoethane)-carbamoyl)cholesterol hydrochloride(DC-Chol); 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP);1,2-dioleoyl-3-dimethylammonium-propane (DODAP);dimethyldioctadecylammonium bromide salt (DDAB);1,2-dilauroyl-sn-glycero-3-ethylphosphocholine chloride (DL-EPC);N-(1-(2,3-dioleyloyx)propyl)-N-N-N-trimethyl ammonium chloride (DOTMA);N-(1-(2,3-dioleyloyx)propyl)-N-N-N-dimethyl ammonium chloride (DODMA);N,N-dioctadecyl-N,N-dimethylammonium chloride (DODAC);N-(1-(2,3-dioleyloxy)propyl)-N-2-(sperminecarboxamido)ethyl)-N,N-dimethylammoniumtrifluoracetate (DOSPA); 1,2-dimyristyloxypropyl-3-dimethylhydroxyethylammonium bromide (DMRIE); dioctadecylamidoglycylspermine (DOGS); neutrallipids conjugated to cationic modifying groups; and combinationsthereof. Non-limiting examples of anionic lipids include fatty acidssuch as oleic, linoleic, and linolenic acids; cholesteryl hemisuccinate;1,2-di-O-tetradecyl-sn-glycero-3-phospho-(1′-rac-glycerol) (Diether PG);1,2-dimyristoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (sodium salt);1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (sodium salt);1-hexadecanoyl,2-(9Z,12Z)-octadecadienoyl-sn-glycero-3-phosphate;1,2-dioleoyl-sn-glycero-3-(phospho-rac-(1-glycerol)) (DOPG);dioleoylphosphatidic acid (DOPA); and1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS); anionic modifyinggroups conjugated to neutral lipids; and combinations thereof.Non-limiting examples of neutral lipids include phosphatidylcholine(PC), phosphatidylethanolamine, ceramide, cerebrosides, sphingomyelin,cephalin, cholesterol, diacylglycerols, glycosylated diacylglycerols,prenols, lysosomal PLA2 substrates, and N-acylglycines. Additionalexamples of lipids and lipid components can be found in U.S. Pat. No.9,833,416.

The lipid nanoparticles can comprise surfactants and/or emulsifiers.Non-limiting examples of surfactants include phospholipids,phosphatidylcholines, TWEENs, Soy lecithin, egg lecithin (Lipoid E 80),phosphatidylcholine, poloxamer 188, 182, and 407, poloxamine 908,Tyloxapol, polysorbate 20, 60, and 80, sodium cholate, sodiumglycocholate, taurocholic acid sodium salt, taurodeoxycholic acid sodiumsalt, butanol, butyric acid, dioctyl sodium sulfosuccinate, andmonooctylphosphoric acid sodium. Non-limiting examples of emulsifiersinclude cationic phospholipid or non-ionic surfactant. Examples ofcationic surfactant include, but are not limited to,1,2-dimyristoyl-3-trimethylammonium-propane (DMTAP),1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP),1,2-distearoyl-3-trimethylammonium-propane (DSTAP),1,2-dioleoyl-3-trimethylammonium-propane (DOTAP),1,2-dimyristoyl-3-dimethylammonium-propane (DMDAP),1,2-dipalmitoyl-3-dimethylammonium-propane (DPDAP),1,2-dilauroyl-3-dimethylammonium-propane (DLDAP),1,2-distearoyl-3-dimethylammonium-propane (DSDAP),dimethyldioctadecylammonium chloride (DDAB),N-[1-(1,2-dioleoyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA)and 1,2-dioleoyl-3-ethylphosphocholine (DOEPC). Examples of non-ionicsurfactants include, but are not limited to poloxamers, sorbitan esters(Span), polyoxyethylene-sorbitan fatty acid esters (Tween) andpolyoxyethylene ethers (Brij).

In certain embodiments, the lipid comprises one or more of: a) cationicor anionic lipids or surfactants; b) neutral lipids or surfactants; c)cholesterol; and d) PEGylated lipids or surfactants.

Other non-limiting examples of lipid-based nanoparticles includeliposomes, bolaamphiphiles, nanostructured lipid carriers (NLC), andmonolayer membrane structures (e.g., archaeosomes and micelles). Methodsof encapsulating agents in lipid nanoparticles are disclosed in Puri etal. Critical Reviews in Therapeutic Drug Carrier Systems 26(6):523-580,2009, the relevant disclosures of which are herein incorporated byreference.

In some embodiments, the TFOs are conjugated to cholesterol to enhancedelivery into cells. In some embodiments, the TFO are administeredabsent of a transport peptide or cell-penetrating peptide (CPP). In someembodiments, the TFOs are administered with a peptide, e.g.,cell-penetrating peptides (CPPs), primary amphipathic peptides, such asMPG or Pep-1.

The administration of the TFOs can be directly to tissue in anindividual. In some embodiments, the TFOs are delivered systemically. Insome embodiments, the TFOs are delivered locally or intratumorally. Insome embodiments, the TFOs are administered as an injection. As used, aninjection can use different delivery routes. In some embodiments, theTFOs are administered intravenously or intraperitoneally. In someembodiments, the TFOs are administered intravenously, intradermally,intraarterially, intralesionally, intratumorally, intracranially,intraarticularly, intraprostaticaly, intrapleurally, intratracheally,intranasally, intravitreally, intravaginally, intrarectally, topically,intramuscularly, intraperitoneally, subcutaneously, subconjunctival,intravesicularlly, mucosally, intrapericardially, intraumbilically,intraocularally, orally, locally, inhalation (e.g., aerosol inhalation),injection, infusion, continuous infusion, localized perfusion bathingtarget cells directly, via a catheter, via a lavage, in creams, in lipidcompositions (e.g., liposomes, lipid nanoparticles, etc.), or by othermethod or any combination of the forgoing as would be known to one ofordinary skill in the art (see, for example, Remington's PharmaceuticalSciences (1990), incorporated herein by reference).

In some embodiments, the TFOs are administered as a composition having apharmaceutically acceptable carrier. In some embodiments, thepharmaceutically acceptable carrier comprises water or saline.

The term “pharmaceutically-acceptable carrier” refers to one or morecompatible solid or liquid filler, diluents or encapsulating substanceswhich are suitable for administration to a human or other subjectcontemplated by the disclosure. “Pharmaceutically acceptable carrier”includes any and all solvents, dispersion media, coatings, surfactants,antioxidants, preservatives (e.g., antibacterial agents, antifungalagents), isotonic agents, absorption delaying agents, salts,preservatives, drugs, drug stabilizers (e.g., antioxidants), gels,binders, excipients, disintegration agents, lubricants, sweeteningagents, flavoring agents, dyes, such like materials and combinationsthereof, as would be known to one of ordinary skill in the art (see, forexample, Remington's Pharmaceutical Sciences (1990), incorporated hereinby reference). Except insofar as any conventional carrier isincompatible with the active ingredient, its use in the therapeutic orpharmaceutical compositions is contemplated.

The TFOs can be administered once, or alternatively they may beadministered in a plurality of administrations. If administered multipletimes, the compounds may be administered via different routes. Forexample, the first (or the first few) administrations may be madedirectly into the affected tissue while later administrations may besystemic.

In some aspects of the present disclosure, the term “individual” refersto a mammal. In some embodiments, individual refers to a human.Alternatively, individual can refer to a mammal, wherein the mammal isselected from a group including but not limited to non-human primates,cows, horses, pigs, sheep, goats, dogs, cats, rabbits, ferrets, androdents. In some embodiments, the term “individual” is used to refer toa model of cancer. Non-limiting examples of models of cancer includep53-knockout mice, BALB/c mice injected with MDA-MB-453 cells, SKBR3cells, BT474 cells, PEO1 cells, or SKOV3 cells, and LFS mouse models(engineered to express mutant p53).

As used herein, the term “sufficient quantity” refers to a“therapeutically effective amount” or “effective amount” that elicits abiological or medicinal response in a tissue, system, animal, individualor human that is being sought by a researcher, veterinarian, medicaldoctor or other clinician. In this case, the response would be areduction (partial or total/complete) in the number of p53-depletedcancer cells comprising a HER2 gene by apoptosis. The appropriateresponse can be determined in vitro by trypsinization and cell counting(using methods established in the art). In vivo, the appropriateresponse from a therapeutically effective amount can be determined bymeasuring or visualizing (e.g., imaging) tumor size.

In some embodiments, the TFOs are administered to an individual in adose of approximately 20 mg/kg. In some embodiments, the TFOs areadministered to an individual in a dose of 5 mg/kg, 7 mg/kg, 9 mg/kg, 10mg/kg, 12 mg/kg, 14 mg/kg, 16 mg/kg, 17 mg/kg, 18 mg/kg, 19 mg/kg, 20mg/kg, 21 mg/kg, 22 mg/kg, 25 mg/kg, or 30 mg/kg. These disclosedamounts can be increased or decreased by one of ordinary skill in orderto personalize a chemotherapeutic treatment plan based on anindividual's stage of cancer, the size of tumor, the presence or absenceof an adjuvant chemotherapeutic agent, etc.

TFO Use for Assays

In alternate embodiments, the method is an assay in which TFOs arecontacted in vitro with p53-depleted cancer cells comprising a HER2gene. As used, the term “contacting” refers to the use of TFOs in invitro assays. The contacting can be through the transfection of cellswith the TFOs in vitro. In some embodiments, the cells are cancer cells.In some embodiments, the cancer cells are contacted with TFOs underconditions under which the TFOs enter the p53-depleted cancer cells insufficient quantity to induce apoptosis under the conditions of the invitro assay.

Methods of transfection are well established in the arts and includechemical, biological, and physical methods. Chemical methods include,but are not limited to, calcium phosphate transfection, cationic polymertransfection (e.g., polyethylenimine), lipofection, Oligofectamine™,DharmaFECT-1™, FUGENE®, and DEAE-Dextran-mediated transfection. Othermethods of transfection include, but are not limited to,electroporation, microinjection, sonoporation, cell squeezing,impalefection, optical transfection, protoplast fusion, magnetofection™,and particle bombardment.

Non-limiting examples of cells that can be contacted by any of the TFOsdescribed herein for in vitro assays, include carcinoma cells, lungcancer cells, colon cancer cells, human colon carcinoma cells, ovariancancer cells, breast cancer cells, colorectal cancer, gastric cancercells, and endometrial cancer cells. Additional non-limiting examples ofcells that can be contacted by any of the TFOs described herein for invitro assays, include MDA-MB-453 cells, SKBR3 cells, BT474 cells, PEO1cells, or SKOV3 cells.

Without further elaboration, it is believed that one skilled in the artcan, based on the above description, utilize the present invention toits fullest extent. The following specific embodiments are, therefore,to be construed as merely illustrative, and not limitative of theremainder of the disclosure in any way whatsoever. All publicationscited herein are incorporated by reference.

EXAMPLES Materials and Methods

Oligonucleotides. Oligonucleotides were synthesized by IDT with a3′-amino modifier and purified by reverse-phase HPLC. The TFO, HER2-1was designed to bind to the HER2 promoter and had the sequence5′-GGGAGGAGGAGGTGGAGGAGGAAGAGGA-3′ (SEQ ID NO: 3). HER2-205 wassynthesized with the sequence 5′-GAG GAG GAG TGG GAG AAT GGG GGG-3′ (SEQID NO: 4) and has been designed to bind to a polypurine sequence in thecoding region of the HER2 gene. The control mixed-sequenceoligonucleotide MIX24 has the following sequence: 5′-AGT CAG TCA GTC AGTCAG TCA GTC-3′ (SEQ ID NO:9). Labeled oligonucleotide was synthesizedwith 5′-TAMRA modifications. HER2-5922-2 was synthesized with thesequence 5′-GGGAAAGAGGAGGGGGTGAGAGGAGTGGGG-3′ (SEQ ID NO: 7). HER2-40118was synthesized with the sequence 5′-GGGGGAAATAGGGAGGGTGGGG-3′ (SEQ IDNO: 8).

Cell Lines and Transfections. Human breast cancer cell lines wereobtained from ATCC and routinely tested for mycoplasma. The human celllines, MDA-MB-453, SKBR3, and BT474 are HER2-amplified breast cancercell lines. BT20 and MCF7 cells are non-amplified breast cancer celllines. MCF-10A is a non-tumorigenic breast epithelial cell line. PEO1and SKOV3 are human ovarian cancer cell lines with HER2 geneamplification.

Cells were seeded in six-well plates at a density of 2-4×10⁵ cells perwell the day before transfection. Cells were transfected with 2 μg ofHER2-targeted TFO or MIX24 using Oligofectamine (Invitrogen) orDharmafect-1 (Dharmacon) transfection reagent. Transfection wasperformed as per manufacturer's instructions. siRNA directed againstp53, XPD and non-target controls (ON-Target plus SMARTpool reagents;Dharmacon) were transfected into BT474 cells using Dharmafect-1transfection reagent (Dharmacon) according to the manufacturer'sinstructions. Western blot analysis was used to confirm knockdown ofprotein.

Metaphase Chromosome Spreads. Cells were transfected with 2 μg of TAMRAlabeled HER2-205. Twenty-four hours post-transfection, cells weretreated for 5 h with Colcemid (0.1 μg/μl). Cells were then collected andwashed once with PBS. To the cell pellet a 75 mM KC1 solution was addedfor 20 minutes at 37° C. Cell pellets were then resuspended in Carnoy'sfixative solution (75% methanol, 25% acetic acid). Following 10 minutesincubation at room temperature, the cells were pelleted and resuspendedin an additional 500 μl of Carnoy's fixative solution (3:1methanol:acetic acid). Cells were dropped from a height onto glassslides and mounting medium with DAPI (Prolong Gold antifade reagent,Invitrogen) was added to each slide. A FITC labeled satellite probespecific for human chromosome 17 (Cytocell) was used to detectgene-specific triplex formation. Pictures were taken of 50-60 metaphasespreads using an Axiovert 200 microscope (Carl Zeiss Micro Imaging,Inc.).

Western blotting. Whole cell lysates were prepared from floating andadherent cells using RIPA buffer according to standard protocols. Totalprotein (30-50 μg per sample) was resolved by SDS-PAGE. Proteins weredetected by a standard immunoblot protocol using the following primaryantibodies: cleaved PARP, cleaved caspase 3, γH2AX, XPD, p53, HER2,pHER2 (Y11221/1222), HER3, pHER3 (Y1289), HER4, pHER4 (Y1284), EGFR,pEGFR (Y1068), Chk1, pChk1(S345), pChk2 (T68), and Chk2 (Cell SignalingTechnology); pH2AX (tyrosine 142; EMD Millipore); tubulin (clone B-512;Sigma), and GAPDH-HRP (Proteintech). Each experiment was repeated withindependent sample preparation a minimum of three times, andrepresentative western blots are shown.

Apoptosis analysis. Cells (2-4×10⁵) were seeded in six-well plates 24 hprior to treatment with MIX24, HER2-1 or HER2-205 (2 μg). Post-treatmentanalysis was performed using the Annexin V-FITC/PI apoptosis detectionkit (BD Pharmingen) according to the manufacturer's protocol. Apoptoticfrequency was calculated as the combined percentage of early and lateapoptotic cells. Data analysis was performed using FlowJo software.

Immunofluorescence. Cells were seeded onto UV-irradiated coverslips andwere treated for 24 h with HER2-205, MIX24, or a mock transfection.Cells were processed 24 h post-transfection, fixed with 4% formaldehydeand then incubated with ice-cold 100% methanol for 20 minutes followedby a methanol and acetone solution (1:1) for 20 minutes each at -20° C.After washing with PBS, cells were blocked with blocking buffer (4% BSA,0.2% Triton X-100 in PBS) for 30 minutes and then incubated overnightwith the following primary antibodies: γH2AX (1:500; Cell Signaling orMillipore) and 53BP1 (1:100; Santa Cruz) in blocking buffer at 4° C.After three washes, cells were incubated with secondary antibodies Alexa488 F(ab′)2 fragment goat anti-rabbit IgG or Alexa 568 F(ab′)2 fragmentgoat anti-mouse IgG (1:1000; Molecular Probes) for 1 h at roomtemperature. Cells were then mounted on microscope glass slides withanti-fade mounting media containing DAPI (Life Technologies), andpictures were taken with a Leica SP5 microscope. Immunofluorescenceexperiments were repeated for validation.

Comet Assay. Neutral comet assays were performed 24 h postTFO-transfection as per the manufacturer's instructions (Trevigen) withthe adjustment of 3.5×10⁵ cells/ml for each single cell suspension and30 minutes electrophoresis. Comets were visualized using an Axiovert 200microscope and analyzed with Autocomet software. Approximately 100-200comets were analyzed per experiment. Results were expressed as mean tailmoment.

Mouse Models. All mice were maintained at Yale School of Medicine inaccordance with guidelines of the Animal Care and Use Committee of YaleUniversity and conformed to the recommendations in the Guide for theCare and Use of Laboratory Animals (Institute of Laboratory AnimalResources, National Research Council, National Academy of Sciences).

Six to seven-week old female BALB/c athymic, ovariectomized nude mice(Harlan Sprague-Dawley) were implanted with 0.72 mg, 60-day release17β-estradiol pellets (Innovative Research). The following day 2.5×10⁷BT474 cells suspended in 100 μl equal volume of media and MatrigelBasement Membrane Matrix (BD Bioscience) were injected subcutaneously inthe right flank of each mouse. Mice bearing a tumor of about 100 mm³ involume were randomly divided into four treatment groups: vehicle (PBS);mixed-sequence oligonucleotide, MIX24; HER2-targeted TFO, HER2-205; andtrastuzumab (HERCEPTIN®). Mice were treated with 20 mg/kg body weight ofMIX24, HER2-205 or trastuzumab in PBS by intraperitoneal (IP) injection(3 doses evenly administered over 7 days). Tumor volumes in each groupwere then monitored and mice were sacrificed when tumor volumes reached1000 mm³. Error bars represent standard error of the mean. Tumortripling time was calculated as the time required for tumors to increasein volume three-fold over baseline (defined as tumor volume beforeadministration of dose on first day of treatment). Harvested tumors werefixed in 10% neutral buffered formalin and processed by Yale PathologyTissue Services for H&E, Caspase 3, HER2, and Ki67. Images were taken at4× magnification.

To establish an ovarian cancer model, female BALB/c athymic nude micewere injected subcutaneously in the flank with 5×10⁶ SKOV3 cellssuspended in 100 μl equal volume of media and Matrigel. Mice bearing atumor of about 100 mm³ in volume were randomly divided into threetreatment groups: vehicle (PBS), n=5; HER2-targeted TFO, HER2-205, n=5;and cisplatin, n=7. HER2-205 (20 mg/kg) and cisplatin (10 mg/kg) wereadministered by intraperitoneal injection (3 doses/once per week forthree weeks). Tumor volumes were monitored and tumor tripling times werecalculated as described above.

Gene Expression. RNA was extracted from snap-frozen cells using theRNeasy Kit (Qiagen) per the manufacturer's protocol. cDNA synthesis wascarried out with 10 μg of RNA via reverse transcription reactions andthe High-Capacity cDNA Reverse Transcription Kit (ThermoFisherScientific). cDNA (10 ng) was then combined with TaqMan Universal PCRmaster mix (20 μl) (Applied Biosystem) and primers specific to HER2(HER2, Hs01001580_ml, ThermoFisher Scientific) or the internal control,β-actin (Hs99999903_ml, ThermoFisher Scientific). qRT-PCR was performedin 96-well optical plates in triplicate for each sample. Briefly,reactions were performed at 50° C. for 2 minutes, followed by 95° C. for10 minutes. Amplification of the target or control gene was carried outwith 40 cycles of the two-step reaction, which included 95° C. for 15seconds and 1 minute at 60° C. β-actin expression levels were used tonormalize the difference between cDNA levels in different samples.Relative expression levels were calculated using the 2(-Delta DeltaC(T)) method.

Flow Cytometry. BT474 cells were collected 24 h following treatment witheither MIX24 or HER2-205. After washing with PBS, cells were incubatedwith 1% paraformaldehyde for 15 minutes on ice. Cells were then fixedwith cold 70% ethanol at −20 ° C. for 2 h or kept for up to 2 weeksuntil further analysis. Cells were centrifuged and rinsed with PBS,blocked with PBST buffer (1% w/v bovine serum albumin and 0.2% v/vTriton X-100 in PBS) for 15 minutes on ice, followed by another PBSrinse. Cells were first incubated with anti-phospho-ATM (S1981, EMDMillipore) in PBST at 1:100 dilution for 1 h at room temperature. Cellswere rinsed with PBST and incubated with anti-rabbit IgG Fab2 Alexa 488(Molecular Probes) at 1:100 dilution at room temperature for 1 h, andthen rinsed with PBST. Acquisition of labeled cells and analysis of datawas completed using a flow cytometer (FACS Calibur) and FlowJo softwarerespectively.

Survival Assay. Cell survival was assayed by visualization of monolayergrowth. Briefly, cells were plated at a defined density in 6 or 12-welldishes and treated with either transfection reagent alone (mock), MIX24,or HER2-205 as previously described. Monolayers were visualized bystaining cells with crystal violet 72 h post-treatment.

Fluorescence in situ Hybridization (FISH). HER2 and chromosome 17 probeswere obtained from Cytocell. The HER2 gene (17q12) probe was labeledwith fluorescent Texas Red spectrum and the CEP17 (17p11.1-q11.1) probewas tagged with FITC. PEO1 and SKOV3 cells were treated with colcemid(0.1 μg/ml) for three hours and collected by trypsinizing the monolayer.After washing the cells with PBS, cells were treated with a hypotonicsolution (0.075 M KC1) at 37° C. for 20 minutes. Cells were then washedand fixed with Carnoy's fixative solution (methanol and acetic acid in3:1 ratio). Cells were dropped on slides and fluorescent in situhybridization was performed on the spreads as per the manufacturer'sinstructions. Images were obtained using a Zeiss microscope with Metafersoftware. A minimum of 50 cells were scored to quantify HER2 andchromosome 17 positive foci.

Statistical analysis. Statistical analysis was performed by one-way ortwo-way ANOVA with the Tukey's test as post hoc. All analysis wascompleted using GraphPad Prism software. Herein, **** denotes p<0.0001,*** denotes p<0.001, ** denotes p<0.01, and * denotes p<0.05.

Results (A) Targeting Gene Amplification in Cancer via Triplex Formation

The present disclosure relates to a promising drug platform thatdirectly converts the amplified oncogenic driver genes into DNA damageto trigger cell death (FIG. 1A). This approach employs TFOs thatrecognize unique polypurine sites within the amplified chromosomalregion. First, a TFO, HER2-1, was designed to target the polypurinesequence in the promoter region of the HER2 gene at positions −218 to−245 relative to the transcription start site (FIG. 1D). Anotherpolypurine site favorable for high affinity triplex formation is locatedwithin the coding region beginning at position 205 and was targeted byanother TFO, HER2-205 (FIG. 1D). Chromosomal TFO binding was confirmedby preparing non-denatured metaphase spreads from MCF7 and BT474 breastcancer cells that had been treated with TAMRA-labeled HER2-205. Thegeneration of chromosomal HER2-205 foci represent third strand bindingto fixed chromosomes with intact DNA double helix¹⁵. Gene-specifictriplex formation was verified using a FITC labeled satellite probespecific for human chromosome 17 (FIG. 1E). TAMRA-HER2-205 chromosomalfoci were only generated on chromosome 17, the location of the HER2gene, thus validating target site specificity (FIG. 1E).

(B) The Level of Triplex-Induced DNA Damage Correlates with Higher GeneCopy Numbers

A neutral comet assay showed that HER2-205 induced significantly moreDSBs in cell lines containing multiple copies of the HER2 gene asindicated by an increase in DNA tail moment (FIGS. 2A-2B). Importantly,the level of triplex-induced DNA damage was directly proportional togene copy number (FIG. 2C). There was also a markedly increased numberof γH2AX positive cells, indicative of DSBs, upon treatment of breastcancer cells with high HER2 gene copy numbers (FIG. 2D). Then 53BP1foci, which colocalize with γH2AX at damage sites, were furtherassessed. HER2-205 treated BT474 cells exhibited substantially increasedγH2AX and 53BP1 foci compared to cells treated with the controloligonucleotide MIX24 (FIG. 2E). Furthermore, colocalization of γH2AXand 53BP1 was observed in 49% of cells following HER2-205 treatment(FIG. 3A).

An experiment was conducted to determine whether HER2-targeting TFOswould be capable of inducing apoptosis specifically in amplified breastcancer cells. The results revealed TFO-induced apoptosis specifically inthe HER2-positive cell lines and that HER2-205 treatment resulted in ahigher percentage of apoptotic cells than that with HER2-1 (FIGS. 2F-2Gand FIG. 3B). Together, the results demonstrate that the intensity oftriplex-induced DNA damage and apoptosis is dependent on gene copynumber (FIG. 2C and 2G). Furthermore, these findings indicate thattriplex-induced apoptosis provides the basis to develop noveltherapeutics that specifically target amplified cancers, while sparingnormal non-amplified tissues.

(C) HER2-205 Treatment Effectively Targets HER2 Positive Ovarian Cancers

The therapeutic efficacy in HER2-positive ovarian cancers was evaluated.When administered to PEO1 and SKOV3 cells, both of which have HER2 copynumber gains (FIG. 3C), HER2-205 treatment induced increased γH2AX fociand DNA tail moments (FIGS. 3D-G). There were also elevated levels ofunrepaired DSBs in the untreated PEO1 cells, which harbor a deficiencyin BRCA2, a key factor involved in DSB repair by homologousrecombination (FIGS. 3F and 3G). Importantly, TFO treatmentsignificantly increased the level of DSBs above baseline (FIG. 3G). Inaddition, HER2-205 reduced cell viability (FIG. 3H) and activatedapoptosis in both cancer cell lines (FIGS. 2H and 3I).

(D)Active HER2-Targeted TFO Could Potentially be used Clinically toTreat HER2-Positive Cancers

To test whether active HER2-targeted TFO could be used clinically totreat HER2-positive cancers in a preclinical model, two independentsubcutaneous xenograft tumor models were developed. Treatment of BT474human breast cancer tumors in athymic nude mice with HER2-205 suppressedtumor growth to a significantly greater degree than the controls,vehicle, and MIX24 (FIGS. 4A and 4C). IP administration of HER2-205resulted in a notable reduction in tumor growth that was comparable tothe currently used targeted therapy trastuzumab, thus demonstrating thepotential utility of this gene-targeted cancer therapy (FIGS. 4A-4B). Atumor tripling time of 29±5.7 days post-initial dose was observed intumors treated with HER2-205 compared to 24±2.1 days in tumors treatedwith trastuzumab (FIG. 4D). In contrast, the control oligonucleotide,MIX24 had no impact on BT474 tumor growth relative to the control bufferalone, with a tumor tripling time for control tumors of 15.7±4.9 daysversus 16.3±6.6 days in tumors treated with MIX24 (ANOVA, p=0.99; FIG.4D). Histological and immunohistochemical analyses were performed onparaffin-embedded tumor tissue sections. Tumor cell apoptosis (evidencedby the presence of cleaved caspase 3), decreased proliferation asmeasured by Ki67 staining, and a confluent area of tumor necrosis wereobserved in the HER2-205 treated specimen (FIG. 4E). Magnification ofthe HER2-205 treated tumor revealed that areas of tumor cell apoptosisare accompanied by a brisk infiltrate of inflammatory cells consistingpredominantly of neutrophils and macrophages (FIG. 4F).

The standard of care for epithelial ovarian cancers consists ofplatinum-based chemotherapy and surgical cytoreduction ²⁰. However, asin the case of the SKOV3 cell line, many human ovarian cancers areresistant to platinum-based drugs. Using SKOV3 ovarian cancerxenografts, we find that HER2-205 treatment showed a substantialsurvival advantage compared with cisplatin (FIG. 4G). HER2-205demonstrated significant tumor growth inhibitory activity with theaverage tumor volume being 49% smaller than those in cisplatin-treatedmice (ANOVA, p=0.006). These data demonstrate that triplex-inducedapoptosis may provide a feasible therapeutic alternative for drugresistant cancers with copy number gains.

(E) Apoptosis Corresponds with the Phosphorylation of Specific DNADamage Response Proteins and XPD is Required for the Induction ofApoptosis

Given that the novelty of the approach herein is based upon thedevelopment of agents with a unique mechanism of action, the status ofDNA damage response proteins, including ATM, Chk1/Chk2, and the NERfactor, XPD in HER2 positive cells was determined following HER2-205treatment. As shown in FIG. 5A, Chk1 phosphorylation at serine 345 wasobserved after HER2-205 treatment in the HER2-amplified cells and not inthe cells with normal HER2 gene copy numbers. Chk1 activation in BT474cells corresponds to induction of DSBs and apoptosis as determined byWestern blot analysis of pH2AX 5139 and cleaved PARP, respectively. Inaddition, phosphorylation of Chk2 at threonine 68 was observed inresponse to triplex-induced DSBs in the BT474 cells (FIG. 5A). Thesephosphorylation events correspond to an increase in pATM positive cellsfollowing HER2-205 treatment (FIG. 6A).

(F) HER2-205 Treatment Activates p53-Independent Apoptosis

To test whether triplex-induced DNA damage could activatep53-independent apoptosis, p53-depleted BT474 cells were treated withHER2-205. The results showed that TFO-treatment of p53-depleted cellsresults in a similar level of PARP cleavage compared to treatment ofcontrol cells, confirming that triplex formation can activate apoptosisirrespective of p53 status (FIG. 5C). Unlike XPD-depleted cells, whichdisplayed a decrease in TFO-induced apoptosis we also demonstrate thattriplex-induced DSBs trigger robust H2AX Y142 phosphorylation in theabsence of p53 (FIG. 5C).

Regulation of the phosphorylation status of H2AX at tyrosine 142 (Y142)is crucial for determining the recruitment of either DNA repair orpro-apoptotic factors to the DSBs site²¹. H2AX Y142 was found tophosphorylate in response to HER2-205 induced DSBs to trigger apoptosisas indicated by Western blot analysis of cleaved PARP (FIG. 5B). XPDoccupies a central role in the mechanism that modulates survival/deathdecisions in response to triplex-induced DNA damage¹⁵. Accordingly, arequirement for XPD in the phosphorylation of Y142 in H2AX andactivation of apoptosis following HER2-205 treatment was seen (FIG. 5B).These results suggest that the absence of XPD disrupts the signalingpathway used to activate apoptosis following TFO treatment and support amechanism of action that is dependent upon DNA damage response.

(G) HER2-Targeted TFO Treatment is Independent of HER 2 Gene Expressionand Cellular Function

Trastuzumab's anticancer activity has been attributed in part to changesin HER2 tyrosine phosphorylation and downregulation of totalHER2^(22,23). To further demonstrate that HER2-205 activity is based ona mechanism independent of the receptor's cellular function, HER2 geneexpression was analyzed by RT-PCR (FIG. 5D) and total HER2 protein andphosphorylation levels were monitored by Western blot followingtreatment in several breast cancer cell lines (FIG. 5E). The resultsshowed that HER2 gene expression is not significantly affected byHER2-205 treatment in either the non-amplified or amplified breastcancer cell lines (FIG. 5D) and that total and activated HER2 levelsremain the same following triplex-induced apoptosis in the HER2-positivecells compared to the control samples (FIG. 5E). In general, no changeswere noted in the levels of HERS, HER4 and EGFR following drug treatmentcompared to the untreated or MIX24 treated cells (FIGS. 6B-6D). Whencombined, these studies revealed no consistent evidence of an alterationof the expression or phosphorylation of HER2 or the HER2 familyreceptors due to drug treatment, thus supporting a mechanism of actionthat is independent of HER2 cellular function and dependent on DNAdamage response (FIG. 5F).

(H) TFOs Designed to Target Non-Coding Regions of HER2 Gene Induce DNADouble Strand Breaks

A neutral comet assay was conducted on BT474 cells 24 hourspost-treatment and showed that the TFOs targeting the non-coding regionsof HER2 (HER2-5922-2 and HER2-40118) and the TFO targeting the codingregion of HER2 (HER2-205) induced significantly more DSBs in cell linescontaining multiple copies of the HER2 gene as indicated by an increasein DNA tail moment (FIG. 8A).

(I) TFOs Designed to Target Non-Coding Regions of the HER2 Gene ActivateApoptosis

Triplex-induced apoptosis of BT474 cells was measured by Annexin-Vstaining. Cells were stained 24 hours post-treatment and the resultsrevealed that TFOs targeting non-coding regions of the HER2 gene caninduce. HER2-40118 and HER2-5922-2 TFOs had more than 2-fold thepercentage of apoptotic cells 24 hours post-treatment (FIG. 8B).

Discussion

Herein, HER2-205 treatment of HER2-positive breast cancer xenograftsresulted in a 52% reduction in tumor volumes compared to controls, whichis comparable to the 58% reduction observed with a currentHER2-associated chemotherapeutic drug, trastuzumab. TFOs targeting thecoding and non-coding regions can induce DNA double strand breaks andapoptosis. Notably, it was confirmed that triplex formation can activatep53-independent apoptosis, which is especially important since p53mutations are associated with therapeutically challenging cancers. Thecompositions and methods disclosed herein can be used as drug designplatform and treatment option for several cancers with geneamplification and resistance to currently used targeted-therapies.

OTHER EMBODIMENTS

All of the features disclosed in this specification may be combined inany combination. Each feature disclosed in this specification may bereplaced by an alternative feature serving the same, equivalent, orsimilar purpose. Thus, unless expressly stated otherwise, each featuredisclosed is only an example of a generic series of equivalent orsimilar features.

From the above description, one skilled in the art can easily ascertainthe essential characteristics of the present invention, and withoutdeparting from the spirit and scope thereof, can make various changesand modifications of the invention to adapt it to various usages andconditions. Thus, other embodiments are also within the claims.

Equivalents

While several inventive embodiments have been described and illustratedherein, those of ordinary skill in the art will readily envision avariety of other means and/or structures for performing the functionand/or obtaining the results and/or one or more of the advantagesdescribed herein, and each of such variations and/or modifications isdeemed to be within the scope of the inventive embodiments describedherein. More generally, those skilled in the art will readily appreciatethat all parameters, dimensions, materials, and configurations describedherein are meant to be exemplary and that the actual parameters,dimensions, materials, and/or configurations will depend upon thespecific application or applications for which the inventive teachingsis/are used. Those skilled in the art will recognize, or be able toascertain using no more than routine experimentation, many equivalentsto the specific inventive embodiments described herein. It is,therefore, to be understood that the foregoing embodiments are presentedby way of example only and that, within the scope of the appended claimsand equivalents thereto, inventive embodiments may be practicedotherwise than as specifically described and claimed. Inventiveembodiments of the present disclosure are directed to each individualfeature, system, article, material, kit, and/or method described herein.In addition, any combination of two or more such features, systems,articles, materials, kits, and/or methods, if such features, systems,articles, materials, kits, and/or methods are not mutually inconsistent,is included within the inventive scope of the present disclosure.

All definitions, as defined and used herein, should be understood tocontrol over dictionary definitions, definitions in documentsincorporated by reference, and/or ordinary meanings of the definedterms.

All references, patents and patent applications disclosed herein areincorporated by reference with respect to the subject matter for whicheach is cited, which in some cases may encompass the entirety of thedocument.

The indefinite articles “a” and “an,” as used herein in thespecification and in the claims, unless clearly indicated to thecontrary, should be understood to mean “at least one.”

The phrase “and/or,” as used herein in the specification and in theclaims, should be understood to mean “either or both” of the elements soconjoined, i.e., elements that are conjunctively present in some casesand disjunctively present in other cases. Multiple elements listed with“and/or” should be construed in the same fashion, i.e., “one or more” ofthe elements so conjoined. Other elements may optionally be presentother than the elements specifically identified by the “and/or” clause,whether related or unrelated to those elements specifically identified.Thus, as a non-limiting example, a reference to “A and/or B”, when usedin conjunction with open-ended language such as “comprising” can refer,in one embodiment, to A only (optionally including elements other thanB); in another embodiment, to B only (optionally including elementsother than A); in yet another embodiment, to both A and B (optionallyincluding other elements); etc.

As used herein in the specification and in the claims, “or” should beunderstood to have the same meaning as “and/or” as defined above. Forexample, when separating items in a list, “or” or “and/or” shall beinterpreted as being inclusive, i.e., the inclusion of at least one, butalso including more than one, of a number or list of elements, and,optionally, additional unlisted items. Only terms clearly indicated tothe contrary, such as “only one of” or “exactly one of,” or, when usedin the claims, “consisting of,” will refer to the inclusion of exactlyone element of a number or list of elements. In general, the term “or”as used herein shall only be interpreted as indicating exclusivealternatives (i.e. “one or the other but not both”) when preceded byterms of exclusivity, such as “either,” “one of,” “only one of,” or“exactly one of.” “Consisting essentially of,” when used in the claims,shall have its ordinary meaning as used in the field of patent law.

As used herein in the specification and in the claims, the phrase “atleast one,” in reference to a list of one or more elements, should beunderstood to mean at least one element selected from any one or more ofthe elements in the list of elements, but not necessarily including atleast one of each and every element specifically listed within the listof elements and not excluding any combinations of elements in the listof elements. This definition also allows that elements may optionally bepresent other than the elements specifically identified within the listof elements to which the phrase “at least one” refers, whether relatedor unrelated to those elements specifically identified. Thus, as anon-limiting example, “at least one of A and B” (or, equivalently, “atleast one of A or B,” or, equivalently “at least one of A and/or B”) canrefer, in one embodiment, to at least one, optionally including morethan one, A, with no B present (and optionally including elements otherthan B); in another embodiment, to at least one, optionally includingmore than one, B, with no A present (and optionally including elementsother than A); in yet another embodiment, to at least one, optionallyincluding more than one, A, and at least one, optionally including morethan one, B (and optionally including other elements); etc.

It should also be understood that, unless clearly indicated to thecontrary, in any methods claimed herein that include more than one stepor act, the order of the steps or acts of the method is not necessarilylimited to the order in which the steps or acts of the method arerecited.

REFERENCES

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23 Cuello, M. et al. Down-regulation of the erbB-2 receptor bytrastuzumab (herceptin) enhances tumor necrosis factor-relatedapoptosis-inducing ligand-mediated apoptosis in breast and ovariancancer cell lines that overexpress erbB-2. Cancer Research 61, 4892-4900(2001).

1. A method of reducing, in a population of cells, the number ofp53-depleted cancer cells in which a HER2 gene is amplified, the methodcomprising contacting p53-depleted cancer cells with triplex formingoligonucleotides (TFOs) targeted to a polypurine target site in theamplified-HER2 gene, under conditions under which the TFOs enter thep53-depleted cancer cells in sufficient quantity to induce apoptosis. 2.The method of claim 1, wherein the p53-depleted cells are mammaliancells.
 3. (canceled)
 4. The method of claim 1, wherein the polypurinetarget site is/comprises SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 5 or SEQID NO:
 6. 5. The method of claim 1, wherein the TFOs are at least 13nucleotides in length.
 6. (canceled)
 7. (canceled)
 8. The method ofclaim 1, wherein the TFOs comprise at least one of the following: anucleotide sequence at least 90% identical to SEQ ID NO: 3 and/or anucleotide sequence at least 90% identical to SEQ ID NO: 4 and/or anucleotide sequence at least 90% identical to SEQ ID NO: 7 and/or anucleotide at least 90% identical to SEQ ID NO:
 8. 9-13. (canceled) 14.A method of reducing, in a population of cells, the number ofp53-mutated cancer cells in which a HER2 gene is amplified, the methodcomprising contacting p53-mutated cancer cells with triplex formingoligonucleotides (TFOs) targeted to a polypurine site in theamplified-HER2 gene, under conditions under which the TFOs enter thep53-mutated cancer cells in sufficient quantity to induce apoptosis. 15.The method of claim 14, wherein the p53-mutated cells are mammaliancells.
 16. (canceled)
 17. (canceled)
 18. The method of claim 14, whereinthe TFOs are at least 13 nucleotides in length.
 19. (canceled) 20.(canceled)
 21. The method of claim 14, wherein the TFOs comprise atleast one of the following: a nucleotide sequence at least 90% identicalto SEQ ID NO: 3, and/or a nucleotide sequence at least 90% identical toSEQ ID NO: 4, and/or a nucleotide sequence at least 90% identical to SEQID NO: 7 and/or a nucleotide at least 90% identical to SEQ ID NO: 8.22-26. (canceled)
 27. A method of treating cancer in an individual withLi-Fraumeni syndrome, the method comprising administering to theindividual TFOs targeted to a polypurine target site in anamplified-HER2 gene, under conditions under which the TFOs enterp53-depleted cancer cells in sufficient quantity to induce apoptosis.28. The method of claim 27, wherein the polypurine target site is SEQ IDNO: 1, SEQ ID NO: 2, SEQ ID NO: 5 or SEQ ID NO:
 6. 29. The method ofclaim 27, wherein the TFOs are at least 13 nucleotides in length. 30.(canceled)
 31. (canceled)
 32. The method of claim 27, wherein the TFOscomprise at least one of the following: a nucleotide sequence at least90% identical to SEQ ID NO: 3, and/or a nucleotide sequence at least 90%identical to SEQ ID NO: 4, and/or a nucleotide sequence at least 90%identical to SEQ ID NO: 7, and/or a nucleotide at least 90% identical toSEQ ID NO:
 8. 33. The method of any one of claims 27 32 claim 27,wherein the TFOs are in a delivery vehicle or are conjugated to adelivery vehicle. 34-40. (canceled)
 41. A method of administering TFOsfor the treatment of cancer, the method comprising: (i) preparing amixture of TFOs targeted to a polypurine target site in anamplified-HER2 gene; and (ii) administering the mixture of TFOs to anindividual, in sufficient quantity to induce p53-independent apoptosis.(iii)

42-58. (canceled)
 59. A composition, comprising: (i) TFOs targeted to apolypurine target site in an amplified-HER2 gene in sufficient quantityto induce p53-independent apoptosis in a p53-depleted cancer cell or ap53-mutated cancer cell; and (ii) a pharmaceutically acceptable carrier.(iii)


60. The composition of claim 59, further comprising: (iii) lipidnanoparticles, wherein the TFOs are encapsulated in the lipidnanoparticles or wherein the TFOs are conjugated to the lipidnanoparticles.
 61. The composition of claim 59, wherein the polypurinetarget site is SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 5 or SEQ ID NO: 6.62. The composition of claim 59, wherein the TFOs are at least 13nucleotides in length.
 63. (canceled)
 64. (canceled)
 65. The compositionof claim 59, wherein the TFOs comprise at least one of the following: anucleotide sequence at least 90% identical to SEQ ID NO: 3, and/or anucleotide sequence at least 90% identical to SEQ ID NO: 4, and/or anucleotide sequence at least 90% identical to SEQ ID NO: 7 and/or anucleotide at least 90% identical to SEQ ID NO:
 8. 66-68. (canceled)